MDA of genomic DNA or circularized bacterial or plasmid DNA can be carried out using random primers at a temperature which is optimal for the DNA polymerase. Generally, this is in a lower temperature range, such as 30-34° C. The DNA to be amplified can be referred to as, for example, the target sequence, template, specific template, input DNA, template DNA, and specific input DNA. The goal of MDA is to amply this input DNA. However, DNA polymerase also can produce undesirable artifacts during these MDA reactions. Such artifacts produced by DNA polymerase and random primers at temperatures that are optimal for the DNA polymerase activity are also observed in other amplification techniques, such as rolling circle amplification (RCA) (examples include multiply-primed RCA, multiply-primed RCA of circular DNA circularized cDNA in isothermal total transcript amplification (ITTA) and multiply-primed RCA of circularized dsDNA using random hexamer and sequence specific primers). The defining characteristic of the artifact DNA is that it does not represent the specific sequence of the input DNA. In fact, the artifact DNA can be produced in the absence of any input DNA (as in the case of control reactions). This is problematic since control reactions lacking input DNA are often carried out with the expectation that no product DNA will be synthesized. Therefore, it would be advantageous to reduce or eliminate the artifact synthesis. Artifact DNA is generally of high molecular weight and therefore is often indistinguishable from the desired specific amplified DNA based on size. In the case where specific input DNA is present, the artifact DNA product can be generated and interferes with the desired use of the specific DNA product, and again, reduction or elimination of artifact production would be beneficial.
In contrast to the low molecular weight artifacts generated during polymerase chain reaction (PCR), referred to as primer dimers, the MDA artifacts are of high molecular weight with lengths ranging from several hundred basepairs to greater than 20 kb. Similar high molecular weight artifacts have also been described for other isothermal amplification systems such as ERCA (PCT/AU99/01110 (Hafner)). Contaminating nucleic acids in DNA polymerase preparations are one of the possible source of undesired template for the generation of these artifacts.